StructureâActivity Relationship of Kahalalide F Synthetic Analogues

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J. Med. Chem. 2008, 51, 4920–4931

Structure-Activity Relationship of Kahalalide F Synthetic Analogues José C. Jiménez,†,‡ Angel López-Macià,‡,§ Carol Gracia,‡ Sonia Varón,‡,| Marta Carrascal,‡ Josep M. Caba,† Miriam Royo,‡,|,⊥ Andrés M. Francesch,§ Carmen Cuevas,§ Ernest Giralt,†,‡ and Fernando Albericio*,†,‡,⊥ Institute for Research in Biomedicine, Barcelona Science Park, Josep Samitier 1, 08028 Barcelona, Spain, Department of Organic Chemistry, UniVersity of Barcelona, Martı´ i Franque´s 1, 08028 Barcelona, Spain, Pharma Mar, S.A., 28770 Colmenar Viejo, Madrid, Spain, Combinatorial Chemistry Unit, Barcelona Science Park, 08028 Barcelona, Spain, and CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine, Barcelona Science Park, Josep Samitier 1-5, 08028 Barcelona, Spain ReceiVed January 26, 2008

Kahalalide F (KF) is a natural product currently under phase II clinical trials. Here, we report the solid phase synthesis of 132 novel analogues of kahalalide F and their in vitro activity on a panel of up to 14 cancer cell lines. The structure-activity relationship of these analogues revealed that KF is highly sensitive to backbone stereotopical modification but not to side chain size modification. These observations suggest that this compound has a defined conformational structure and also that it interacts with chiral compounds through its backbone and not through its side chains. The N-terminal aliphatic acid appears to be a hydrophobic buoy in a membrane-like environment. Moreover, significant improvement of the in vitro activity was achieved. Introduction Kahalalide F (KF,a Figure 1) is a depsipetide that was first isolated in 1993 by Hamman and Scheuer from a marine mollusk, Elysia rufescens, and from the algae that the mollusk feeds on, Bryopsis pennata.1 It has also been reported in another mollusk, Elysia grandifolia.2,3 KF shows in vitro activity against prostate and colon cancer cells and to a lesser extent, antiviral, antifungal, and bactericide activity.4 Two clinical phase I trials in adult patients with advanced prostate cancer and pretreated solid tumors have established the recommended dose for two distinct treatment regimes (once a week and 5 consecutive days * To whom correspondence should be addressed. Phone: 0034 934037088. Fax: 0034 934037126. E-mail: [email protected]. † Institute for Research in Biomedicine. ‡ University of Barcelona. § Pharma Mar, S.A. | Combinatorial Chemistry Unit. ⊥ CIBER-BBN, Networking Centre on Bioengineering, Biomaterials and Nanomedicine. a Abbreviations: Alloc, allyloxycarbonyl; Bip, 2-amino-3-biphenyl-4ylpropionic acid; Boc, tert-butyloxycarbonyl; Bza-OH, benzoic acid; Cha, cyclohexylalanine or 2-amino-3-cyclohexylpropionic acid; p-CF3Bza-OH, 4-trifluoromethylbenzoic acid; p-TflPhAc-OH, 3-(4-trifluoromethylbenzyl)acetic acid; p-TflCinn-OH, 3-(4-trifluoromethylbenzyl)acrylic acid; ClTrtCl-resin, 2-chlorotrityl chloride resin; Dha, 2-aminoacrylic acid; Z-Dhb, R,β-didehydro-R-aminobutyric acid; DIPEA, N,N-diisopropylethylamine; DMF, N,N-dimethylformamide; EDC · HCl, 1-ethyl-3-(3′-dimethylaminopropyl)carbodiimide hydrochloride; Fmoc, 9 fluorenylmethoxycarbonyl; 6,6dFHep-OH, 6,6-difluoroheptanoic acid; 3,5-dFPhAc-OH, (3,5-difluorophenyl)acetic acid; 4-GuBut-OH, 4-guanidinobutyric acid; GI50, growth inhibition at 50%; hCh, homocyclohexylalanine or 2-amino-4-cyclohexylbutyric acid; Hep-OH, heptanoic acid; HOAc, acetic acid; HOAt, 1-hydroxy-7-azabenzotriazole (3-hydroxy-3H-1,2,3-triazolo[4,5-b]pyridine); HOBt, 1 hydroxybenzotriazole; Icos-OH, icosanoic acid; KF, kahalalide F; LC50, lethal concentration at 50%; Lit-OH, litocholic acid; MeHex-OH, methyhexanoic acid; (c/t)-MecHex-OH, (cis/trans)-4-methylcyclohexanecarboxylic acid; p-MeBza-OH, 4-methylbenzoic acid; MeOH, methanol; Mst-OH, myristic acid or tetradecanoic acid; NaI, 2-amino-3-naphthalen-2-ylpropionic acid; Oct-OH, octanoic acid; 6-Ohep-OH, 6-oxoheptanoic acid; Oic, octahydroisoindole-1-carboxylic acid; Phf-OH, perfluoroheptanoic acid; Phg, aminophenylacetic acid; (5R)-Ph-Pro, 5-(R)-phenylpirrolidine-2-carboxilic acid; Pip, pipecolic acid; Pipe-OH, benzo[1,3]dioxole-5-carboxilic acid; SPS, solid-phase synthesis; SRB, sulphorhodamine B; TCA, trichloroacetic acid; Tfa, trifluoroacetyl; TFA, trifluoroacetic acid; TFAA, trifluoroacetic anhydride; TGI, total growth inhibition; Thi, 2-amino-3-thiophen-2-ylpropionic acid; Tic, 1,2,3,4-tetraisoquinoline-3-carboxilic acid; Und-OH, undecanoic acid.

every 3 weeks).5,6 KF phase II clinical trials in hepatocellular carcinoma, non-small-cell lung cancer (NSCLC) and melanoma finished in 2006. Moreover, KF is being tested in phase II clinical trials in patients with severe psoriasis. Phase I trials showed that the dose-limiting toxicity was a reversible elevation of liver transaminases. The mechanism of action of KF is mostly unknown. KF is a National Cancer Institute COMPARE-negative compound, which indicates that its cytotoxicity might be related to a unique mode of action. A first study indicated that cells treated with KF became swollen and developed large vacuoles, which appeared to be a consequence of changes in lysosomal membranes.7 Recently, a further study has revealed that KF induces oncosis8 and that it has a 5to 40-fold greater effect on cancer cells than healthy cells.6,9 The mechanism of action of KF does not affect the nuclear structure of the cell, while the integrity of crucial organelles such as mitochondria, endoplasmic reticulum, and lysosomes is severely compromised. The alterations found indicate that the osmotic balance of the cell may be altered, possibly as a result of cellular membrane damage. Thus, it appears that KF does not induce apoptosis, the main mechanism by which tumor cells are killed by anticancer drugs or radiotherapy.10 Moreover, the mechanism of action of KF is caspase-independent and not affected by DNA expression.8 With the aim to identify new KF analogues with improved pharmacological properties and examine the role of each residue on the biological activity of this compound, our group developed a structure-activity relationship (SAR) program. In order to understand this study, it is noted that the KF structure is divided into three domains: domain A includes the macrocycle; domain B contains the peptide tail; domain C is the N-terminal aliphatic acid (Figure 1). Here, we report the synthesis and in vitro cytotoxicity of 132 KF analogues on several human cancer cell lines. Results and Discussion Synthesis of KF Analogues. The analogues were synthesized following the scheme used for the first KF synthesis with minor modifications (Scheme 1).11,24 These modifications were mainly (i) the use of DIPCDI/HOBt as coupling reagents in the solid-

10.1021/jm8000828 CCC: $40.75  2008 American Chemical Society Published on Web 08/01/2008

Synthetic analogues of Kahalalide F

Journal of Medicinal Chemistry, 2008, Vol. 51, No. 16 4921

Figure 1. KF structure with its three domains highlighted.

Scheme 1. Synthetic Strategies for Solid-Phase Synthesis of KF Analoguesa

a Conditions: (a) Fmoc-D-Val-OH, DIEA, DMF; (b) piperidine-DMF (2:8); (c) Fmoc-aa-OH, DIPCDI, HOBt, DMF; (d) Alloc-Val-OH, DIPCDI, DMAP; (e) 5-MeHex acid, DIPCDI, HOBt, DMF; (f) Pd(PPh3)4, PhSiH3, DCM; (g) Alloc-Phe-(Z)-Dhb-OH, DIPCDI, HOAt, DMF; (h) EDC · HCl, CuCl, DMF-DCM (1:9); (i) TFA-DCM (1:99); (j) DIPCDI, HOBt, DIEA, DCM; (k) TFA-DCM (19:1).

phase elongation (SPPS) instead of azabenzotriazole-based reagents and (ii) the use of DIPCDI/HOBt/DIEA for the cyclization step instead of PyBOP/DIEA. Azabenzotriazole derivatives are expensive, and therefore, their substitution greatly reduces the cost of the synthesis. Moreover, these changes imply that the epimerization on the DVal(4) is prevented during cyclization. For the synthesis of most of the analogues, one or

more amino acids, or the 5-MeHex acid, were either removed or substituted by another properly protected amino acid or acid. In Scheme 1, two alternative routes to incorporate the nonproteinogenic amino acid Z-didehydroaminobutyric acid [(Z)-Dhb] are shown. Route A was chosen for most of the analogues. This procedure involves the incorporation of a presynthesized dipeptide, Alloc-Phe-(Z)-Dhb-OH, to the peptide

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Table 1. Mean Activity of KF in Assay A (Values in Molar (M))

acyclic natural analogue of KF, kahalalide G, it is known that the ring is essential for biological activity.4 The presence of D-amino acids, the non-natural amino acid (Z)-Dhb, and the lack of a C-terminal amino acid as a result of the lactamization confer a high degree of enzymatic stability to this domain.15 These features also increase the rigidity of the domain, which may be of relevance for activity.15 The most explored residue in this domain is Phe (3), with 20 analogues, the most active being those that introduce halogen groups on the aromatic ring, with the greatest of the activity in compounds 22 [Phe(2-Cl)], 23 [Phe(3-Cl)], 24 [Phe(4-Cl)], 25 [Phe(3,4-F2)], and 26 (NaI). Interestingly, 11 [Phe(3,4-Cl2)] with two chlorines on the aromatic ring was not as active as the monochlorinated compounds 22, 23, or 24, and the position of the chlorine did not appear to be relevant. In contrast, 25 [Phe(3,4-F2)] with two fluorines was more active than the analogue with a single fluorine (15) and the analogue with five fluorines (12). The analogues at Phe (3) suggest that a hydrophobic residue is required in that position. Almost all halogen derivatives of Phe were more active than KF. Compounds in which Phe was replaced by Trp (9), hCh (10), and methylated Tyr (16) were more active, while hydrophilic compounds such as Thi (17) and Tyr (19) showed lower activity. Analogues that restricted the rotation of the aromatic ring through N-alkylation either did not improve activity (N-MePhe, 21) or blocked it (Oic 20, Tic 18). Finally, the Phg derivate (28), which can be considered a Phe lacking the β-methylene atom, was slightly less active. Given the ring nature of domain A, the L/D configuration of the R-carbon of the backbone is crucial. Compound 29 explored the possibility of Val(4) instead of D-Val.25 This analogue lost all activity, thereby confirming the importance of the conformation of the cycle. A presumably key amino acid in this domain is (Z)-Dhb. Analogues at this residue included other didehydroamino acids such as (Z)-Dhf (3) and Dha (4). These two compounds were as active as KF, thereby indicating that its role revolves around the rigidness and special configuration that didehydroamino acids confer to the main chain,15 with no major relevance of their side chains. This point could be reinforced by the observation that analogues 1 and 2, which contain L and D ethylglycine (Etg), the saturated versions of (Z)-Dhb, were less active than KF. Analogues 5 and 6, which incorporate D-Thr and D-allo-Thr, respectively, in that position showed almost no activity. Compounds with aquiral amino acids such as Gly (7) and Aib (8) did not show activity either. Finally, the D-allo-Thr that closes the ring was the subject of a set of analogues with D-Dapa (30), D-Thr (31), and D-Ser (32) (30 is the aza version of 32). Analogue 32 (D-Ser) maintained the activity of KF, which could indicate that the β-methyl group of the D-allo-Thr is not relevant for the stabilization of the structure. However, when this methyl group was misplaced in analogue 31, activity was lost. When D-Ser (32) was substituted by D-Dapa (30), activity was lost again. These observations indicate that the pattern of hydrogen bond donors/acceptors or the freedom around the heterodetic bond may be relevant to the conformation. So far, the term “activity” has been referred to the overall activity of the cell lines compared to KF. On closer inspection, we can rank activity depending on the tissue from which the tumor derives. Cell lines were as follows, in order of sensitivity from high to low: colon (HT-29, LOVO and LOVO-DOX), ovary (IGROV and IGROV-ET), breast (SK-BR-3), prostate (DU-145 and LN-caP) and melanoma, lung, bone marrow

prostate ovary breast melanoma lung (NSLC) leukemia pancreas colon cervix

DU-145 LN-caP IGROV IGROV-ET SK-BR3 SK-MEL-28 A549 K-562 PANC1 HT29 LOVO LOVO-DOX HELA HELA-APL

GI50

TGI

LC50

9.31 × 10-7 9.60 × 10-7 4.93 × 10-7 5.50 × 10-7 3.63 × 10-7 1.19 × 10-6 1.16 × 10-6 1.93 × 10-6 1.77 × 10-6 4.32 × 10-7 3.34 × 10-7 2.99 × 10-7 9.65 × 10-7 9.75 × 10-7

1.72 × 10-6 1.96 × 10-6 1.18 × 10-6 1.30 × 10-6 8.10 × 10-7 2.26 × 10-6 2.20 × 10-6 3.32 × 10-6 3.33 × 10-6 9.15 × 10-7 6.14 × 10-7 4.85 × 10-7 1.97 × 10-6 2.02 × 10-6

3.72 × 10-6 4.26 × 10-6 3.22 × 10-6 3.28 × 10-6 1.98 × 10-6 4.50 × 10-6 4.52 × 10-6 5.28 × 10-6 5.07 × 10-6 2.24 × 10-6 1.51 × 10-6 1.47 × 10-6 4.73 × 10-6 4.29 × 10-6

sequence as a regular amino acid. Route B, which involves a β-alcohol solid-phase dehydration, takes longer and gives a lower yield12 and was therefore used only when the modification was on the amino acids (Z)-Dhb or Phe. Finally, another set of analogues was obtained by reaction of KF or an intermediate with diverse reactants through the amino group of Orn (acylation with common coupling reagents) or the hydroxyl group of Thr (acylation with DIPCDI in the presence of DMAP).13 Antitumoral Screening and Data Representation. The cytotoxicity of each peptide was evaluated against a panel of up to 14 human tumor cell lines. The cytotoxic assay (assay A in methods section) gives an output of three parameters: GI50 (concentration at which the growth is inhibited by 50%), TGI (concentration at which the growth is totally inhibited), and LC50 (lethal concentration that will kill 50% of the cells).14 Of these parameters, only GI50 is shown in Tables 2–5 to facilitate comparison. The mean activity for KF is shown in Table 1. Moreover, the activity of several analogues was taken from another assay (assay B in methods section), which was performed at the very beginning of this study. The output data of this assay is the IC50 (half-maximal inhibitory concentration). Compounds that did not show relevant activity were not tested again in assay A. For the sake of simplicity, the activity of these compounds has been included in the table with the other analogues and can be distinguished by an asterisk. Activity data are shown in Tables 2–5 using a color palette to describe GI50 concentration in a logarithmic scale. SAR. From the 132 KF analogues synthesized and tested, 32 had modifications at domain A (analogues 1-32, Table 2), 59 at domain B (33-91, Table 3), and 34 at domain C (analogues 92-125, Table 4). In addition, seven had modifications in more than one domain (analogues 126-132, Table 5). The chemical structure of each substitution is given in Figures 24. Several compounds in Tables 2 (domain A) and 3 (domain B) had two modifications on their structure: one related to the explored domain and the other corresponding to the N-terminal moiety. The 5-MeHex in these compounds was substituted by 4(S)-MeHex in position 14. This switching did not affect the in vitro activity, as demonstrated in parallel experiments that showed that these two acids led to similar in vitro activity. In contrast, the compound with 4(S)-MeHex (100, Table 4) exhibited higher in vivo efficacy in breast and prostate xenografts.19 Domain A Analogues. This domain contains the macro ring formed by the six C-terminal amino acids closed by an ester bond between the carboxylic acid of Val (1) and the β-hydroxyl function of D-allo-Thr (6). Given the absence of activity of the



Table 2. Domain A KF Analoguesa

a The chemical structure of each modification can be found in Figure 2. “4” in 5-MeHex column indicates the presence of 4(S)-MeHex. Colored squares represent the GI50 (or IC50 on marked (/) compounds) of each compound on the cells lines tested. Colored values at the bottom are expressed in mol/L.

(leukemia), and pancreas (MEL-28, A-545, K-562, and PANC1). Depending on the analogue, this selectivity was altered; for example, for 9 (Trp3), selectivity for ovary cell lines was greater than for colon. For 11 [Phe(3,4-Cl2)] the selectivity for lung cell line was increased. For 27 (Bip3) the activity in lung was higher than in any other cell line. Domain B Analogues. This domain is composed of seven amino acids. It is rich in aliphatic residues including a D-alloIle, three Val (two D and one L), and one D-Pro. The domain is completed with one Thr and one Orn, which is the only charged amino acid in the peptide at physiological pH. It is also noticeable that four of the residues have configuration D. All analogues in which the chirality of any residue was switched lost their activity [Table 3, analogues 54 (Pro), 66 (DVal11), and 76 (D-Thr)] except for 86 (Val13), which is the closest residue to the N-terminal aliphatic acid. The importance of the configuration of the R carbons of the amino acids suggests that this domain is not merely a link without structure between the other two domains but rather adopts or induces some sort of folding and/or interactions with another molecule. One set of compounds we synthesized explored the elimination of residues starting from D-allo-Ile 7 (analogues 46-52). None of these analogues showed activity. In all these analogues the positive charge of Orn was missing, which may explain the loss of activity. To confirm this assumption, we synthesized compound 53 in which the Orn was kept but the last three residues were removed. This synthesis resulted in no activity.

To confirm that the loss of activity was not induced by the loss of the total chain length, compound 130 (Table 5), which included the C14 myristic acid at the N-terminus, was also explored simulating the approximate length of the total chain. This also resulted in no activity. These observations corroborate the need for chiral information on that part of the peptide. Moreover, when a residue was substituted by a distinct amino acid, the activity was conserved or even increased when nonpolar amino acids with the same chirality were used (analogues 59, 63, 65, 73, 75, 81, 83, 85, and 87). The exception to this observation was, again, at position 13, where D-Val could not be replaced by the more hindered amino acid D-Cha (analogues 60 and 61). It is also of note that the hydroxyl group of the Thr was not required for antitumoral activity. Furthermore, the activity was increased with aliphatic substitutions (analogues 63 and 65). The substitution of D-Pro by L-Pro (54) and (R)-5Ph-L-Pro (57) led to no activity, pointing again to the existence of some sort of folding or recognition. Moreover, neither did the substitution by six-member ring D-Pro analogues D-Pip (55) and D-Tic (56) produce activity, which introduces another twist to the peptide conformational sensitivity in that region, since increasing from five- to sixmember ring had less impact on the orientation of the groups than changing the chirality of the amino acid. Compound 58 has historical relevance in the determination of KF structure. The first report on KF stereochemistry assigned the configurations D and L to Val (10) and Val (11), respec-


Jiménez et al.

Table 3. Domain B KF Analoguesa

a The chemical structure of each modification is shown in Figure 3. “4” in 5-MeHex column indicates the presence of 4(S)-MeHex. “no” indicates the absence of that residue in the compound. Colored squares represent the GI50 (or IC50 on marked (/) compounds) of each compound on the cell lines tested. Colored values at the bottom are expressed in mol/L.

tively.16 A review of this work originated a second assignment where the stereochemistry in these two residues was switched.17 The two compounds were synthesized and compared to natural KF by NMR and by activity assay, solving the correct assignation without any doubt.11 NMR spectra of these two compounds showed a single set of signals for KF, while analogue 58 presented two sets corresponding to cis/trans Pro isomerization. This was the first example of the sensitivity of the structure of domain B to the stereochemistry of its residues and how these affected its activity. Furthermore, several analogues were prepared by direct reaction on the amino group of Orn in KF with diverse reagents, taking advantage of the regioselectivity of this group over the rest of the molecule as previously done on KF by other groups (analogues 33-39 and 42-44).18 We completed this set with the introduction of distinct amino acids instead of Orn (analogues 40 and 41).

Here, we found the most active compounds, analogues 35 and 37. In general, compounds with aliphatic groups coupled to the amino group of Orn were the most active (34-37). In analogue 37 the activity fell when the Fmoc group was cleaved, thereby generating a positive charge (analogue 38). This is surprising, since this is the only charged amino acid in the whole sequence, and it seems to be not only unnecessary but undesirable. Moreover, these compounds open the door to conjugates with aliphatic drugs at that point that cannot only act in synergy with KF but can also increase its inner activity in the same way as analogues 35 and 37 do. Another important datum is that Lys (40) is as active as Orn. This may seem strange because Lys is a coded amino acid and therefore more likely to be used in a natural product. Recently, it has been reported that this compound is also present (called as kahalalide S) in small amounts in Elysia grandifolia and the algae it feeds on, Bryopsis plumose.3



Table 4. Domain C KF Analoguesa

a The chemical structure of each modification is shown in Figure 4. “no” indicates the absence of that residue in the compound. Colored squares represent the GI50 of each compound on the cell lines tested. Colored values at the bottom are expressed in mol/L.

Table 5. KF Analogues in More Than One Domaina

a The chemical structure of each modification is shown in Figures 2–4. “no” indicates the absence of that residue in the compound. Colored squares represent the GI50 of each compound on the cell lines tested. Color values at the bottom are expressed in mol/L.

The broad range of active compounds modified on Orn suggests that this residue is not involved in any recognition interface. When we examined the changes in cell line selectivity, we observed that the analogues with hydrophobic molecules capping

the δ-amino group of Orn not only were the most active but also showed the most changes in selectivity. Thus, analogue 37 [Orn(Fmoc-PEG)] was as active or even more active on prostate, lung, bone marrow, and pancreas cell lines than on colon, breast, and ovary cell lines. This effect was also observed


Jiménez et al.

Figure 2. Building blocks used for the substitution of residues at domain A.

Figure 3. Building blocks used for the substitution of residues at domain B.

in analogue 35 [Orn(cHP)]. Analogues 33, 36, and 43 increased their activity in breast and colon cell lines with no major effect

on the rest of cell lines. A remarkable case was compound 69 (Orn11 instead of Val). This compound not only broke the rule



Figure 4. Building blocks used for the substitution of residues at domain C.

that aliphatic changes are preferred over polar substitutions but also affected mainly leukemia and showed very low activity against the rest of the panel cell lines. Domain C Analogues. The analogues generated at this domain required an aliphatic group in this position. Any inclusion of polar groups able to generate hydrogen bonds decreased the activity (analogues 117-123). Compounds with no terminal acid (92) or a short aliphatic group (analogues 93-98) had lower activity than KF. Finally, the activity was maintained or increased when the N-terminal acid was substituted by a more aliphatic group (99-116). An exception to this rule was analogue 108 (icosanoic acid, C20), where the low activity can be explained by the poor solubility of the compound. In compound 125 [Lit(OTfa)] the ester group generated hydrogen bonds but the relative size of the molecule must be considered. A practical example of this is the finding of two new natural kahalalides called kahalalide R (KR) and kahalalide S (KS)

found in the organism Elysia grandifolia.2 In KR the 5-methylhexanoic acid in position 14 is substituted by 7-methyloctanoic acid, while in KS it is substituted by 5-hydroxy-7-methyloctanoic acid. KR is as active as KF, while KS is 20-fold less active than KF. It is noted that references 2 and 3 both use letters R and S to describe four new kahalalide compounds. Compounds 100 and 101 showed an interesting effect. These two compounds incorporated the two enantiomers of 4-metylhexanoic acid, which is the compound closest to 5-methylhexanoic acid with a chiral center. The activity of the compound that incorporated the R enantiomer was lower than that which incorporated the S enantiomer, the activity of the latter being similar to the parent peptide. Further in vivo studies on these compounds showed that compound 100 has enhanced efficacy against breast and prostate xenografts.19 On the basis of this observation, we chose to incorporate 4(S)-MeHex instead of 5-MeHex into other analogues.


Several analogues clearly showed higher in vitro activity than the parent peptide. Here, we highlight compounds 102, 104-107, 111, 112, 116, and 125, the most active analogues being 106 (undecanoic acid, Und), 107 (palmitic acid), 112 (pTflBza), 116 (p-TflCinn), and 125 [Lit(OTfa)]. Compounds 111 and 112 were very similar, the only difference being that 112 had a trifluoromethyl group instead of a methyl group attached to the aromatic ring. These two groups exerted an opposite inductive effect on the aromatic ring, with enhanced electronic density on compound 111 and lower electronic density on compound 112, the latter being more active. The wide array of molecules that maintained or increased the activity in domain C and the common characteristic of their high aliphatic behavior suggest that this domain does not interact selectively with any other molecule and that its main function is as an aliphatic buoy. As seen in other domains, a number of compounds showed a change in their selectivity against the cell lines assayed. Analogues 102, 106, 107, 112, 116, and 125 had predominant activity against ovary cell lines. Compound 107 also significantly increased activity against prostate cell lines. Multidomain Analogues. Table 5 shows the analogues modified in more than one domain. The first entry (126) corresponds to the KF enantiomer, which showed no activity. Analogues 127 and 128 showed once again that more hydrophobic residues (D-Cha) than those of Val or Ile increased the activity, and when the number of methylenes was reduced (e.g., substituting D-allo-Ile by Val), the activity diminished. This behavior can also be explained by conformational changes induced by the volume of the side chains, since Val is less voluminous than D-allo-Ile, thereby allowing more conformations. Analogue 129, which is the combination of analogues 11 and 116, showed increased activity compared to KF but not significantly higher than that of compound 11. Finally, in compound 132, the amino group of D-Val13 was alkylated with two heptane chains. This substitution led to no activity, which can be explained by the generation of a very stable positive charge at this nitrogen. In this panel we observed changes in the cell line selectivity of compounds 127, 129, and 131, where again the compounds were most active on ovary cell lines. Also worth mentioning is the increased activity against prostate cell lines in compound 127. In compound 129 the activity against lung cell line (A549) was very high because of the presence of Phe(3,4-Cl2) at the third position, as with compound 11. Conclusions Kahalalide F has a more defined structure than expected. This is not surprising in cyclic domain A, but astonishingly it also occurs in domain B, which a priori is much more flexible. KF is highly sensitive to stereotopical changes, namely, those changes that affect chirality at the R-carbon of the residue. KF is not sensitive to side chain substitutions in almost every residue, the electronic density of the substituting chain being more relevant than its volume. For almost every side chain, it was possible to find a distinct side chain that could preserve or even improve the activity. Our results on enantiomer 126 suggest that KF interacts with at least one chiral compound to develop cytotoxicity. In this regard, we found a more hindered replacement in each side chain able to keep or improve the activity; the interactive region should be pointed at the backbone of the molecule, the cycle being the more appealing target.

Jiménez et al.

The activity can be increased by enhancing the hydrophobicity at any position on the molecule, solubility in water being a limiting factor. Domain C is the most sensitive to this rule, since it does not allow the inclusion of electronic-donor atoms such as oxygen or nitrogen. Domain C accepts only highly hydrophobic groups with a low heteroatom load. This observation suggests that this domain interacts with a highly hydrophobic and unspecific environment such as a membrane, possibly with the lysosomal membrane since KF affects this organule.7 Analogues with a hydrophobic group attached to the ε-amino group of Orn open the door to conjugated drugs (i.e., 33, 34, 35, and 37). These compounds are more active than KF and compounds with polar groups. This finding implies that KF activity can be enhanced while simultaneously using KF as a carrier of a hydrophobic drug with solubility or transport limitations, thereby obtaining a synergic effect. As an extension of the above discussion, we consider this set of analogues to be useful also as control peptides in research into the biological mechanism of KF. By examination of the distinct behavior displayed by some analogues compared to KF, it is possible to identify the role played by each part of the peptide in the overall activity. An example of this approach would be the enantiomer analogue 126. Studying its capacity to internalize the cell would provide information as to whether KF is actively internalized by a carrier or unspecifically internalized. Also relevant, this set of compounds opens up the possibility of modulating KF selectivity when used in distinct cell lines. It would therefore be feasible to develop analogues with different tissue specificity. This would allow the development of KFrelated compounds targeted to a particular kind of tumor, thus obtaining a wider therapeutic window. Finally, now that the impact of backbone stereochemistry on KF activity is known, analogues that affect this stereochemistry can be used to perform structural studies of KF by means of molecular modeling and NMR. These analogues are 1, 2, 3, 7, 8, 30-32 in domain A and 54-58, 62, 66, 76, and 86 in domain B. Experimental Section Cl-TrtCl-resin, protected Fmoc-amino acid derivatives, HOBt, and HOAt were from ABI (Framingham, MA), Bachem (Bubendorf, Switzerland), and NovaBiochem (La¨ufelfingen, Switzerland). 4-MeHex derivatives were from Narchem. HATU was from ABI (Framingham, MA). DIPEA, DIPCDI, EDC · HCl, piperidine, and TFA were from Aldrich (Milwaukee, WI). DMF and CH2Cl2 were from SDS (Peypin, France). Acetonitrile (HPLC grade) was from Scharlau (Barcelona, Spain). All commercial reagents and solvents were used as received with the exception of CH2Cl2, which was passed through an alumina column to remove acidic contaminants. Alloc-amino acids were prepared essentially as described,20 and alloc-Z-Dhb-Phe-OH compounds were prepared as described11 and also in Supporting Information. HRMS was performed in LTQ-FT Ultra from ThermoScientific in nanospray mode by infusion and H2O/CH3CN (1:1) + 0.1% formic acid as a solvent. MALDI-TOF and ES-MS analyses of peptide samples were performed in a PerSeptive Biosystems Voyager DE RP, using DHB matrix, on a Waters Micromass ZQ spectrometer and on an Agilent ion trap 1100 series LC/MSDTrap. Peptide-resinsampleswerehydrolyzedin12NaqueousHCl-propionic acid (1:1) at 155 °C for 1-3 h, and peptide-free samples were hydrolyzed in 6 N aqueous HCl at 155 °C for 1 h. Subsequent amino acid analyses were performed on a Beckman System 6300 autoanalyzer. 1H NMR spectroscopy [1H, NOESY, TOCSY at 278 K] was performed on a Varian Unity Plus (500 MHz). Chemical shifts (δ) are expressed in parts per million downfield from TMS. Coupling constants are expressed in hertz. Analytical HPLC was


carried out on a Waters instrument comprising two solvent delivery pumps (Waters 1525), automatic injector (Waters 717 autosampler), dual wavelength detector (Waters 2487), and system controller (Breeze, version 3.20) and on an Agilent 1100 instrument comprising two solvent delivery pumps (G1311A), automatic injector (G1329A), and DAD (G1315B). UV detection was at 215 or 220 nm, and linear gradients consisted of CH3CN (+0.036% TFA) into H2O (+0.045% TFA). Here, we describe the synthesis of compound 100 as a general example. Detailed synthesis and characterization of the rest of the compounds can be found in Supporting Information. (4S)-MeHex-D-Val-ThrVal-D-Val-D-Pro-Orn-D-allo-Ile-ciclo[Dallo-Thr-D-allo-Ile-D-Val-Phe-(Z)-Dhb-Val], [(4S)-MeHex14]KF, Compound 100. Step 1 of 7. H-D-Val-O-TrtCl-Resin. Cl-TrtClresin (1 g, 1.64 mmol/g) was placed in a 20 mL polypropylene syringe fitted with a polyethylene filter disk. The resin was then washed with CH2Cl2 (5 × 0.5 min), and a solution of Fmoc-DVal-OH (238 mg, 0.7 mmol) and DIPEA (0.41 mL, 2.41 mmol) in CH2Cl2 (2.5 mL) was added. The mixture was then stirred for 15 min. Extra DIPEA was then added (0.81 mL, 4.75 mmol), and the mixture was stirred for 45 min. The reaction was completed by addition of MeOH (800 µL, 19.78 mmol), after stirring for 10 min. The Fmoc-D-Val-O-TrtCl-resin was subjected to the following washings/treatments with CH2Cl2 (3 × 0.5 min), DMF (3 × 0.5 min), piperidine as indicated in the general procedures section, and DMF (5 × 0.5 min). The loading was 0.50 mmol/g calculated by Fmoc determination. Step 2 of 7. Fmoc-D-allo-Ile-D-allo-Thr(Val-Alloc)-D-allo-IleD-Val-O-TrtCl-Resin. Fmoc-D-allo-Ile-OH (707 mg, 2 mmol, 4 equiv), Fmoc-D-allo-Thr-OH (free hydroxy group) (683 mg, 2 mmol, 4 equiv), and Fmoc-D-allo-Ile-OH (707 mg, 2 mmol, 4 equiv) were added sequentially to the H-D-Val-O-TrtCl-resin described above using DIPCDI (310 µL, 2 mmol, 4 equiv) and HOBt (307 mg, 2 mmol, 4 equiv) in DMF (2.5 mL). In all cases, after 90 min of coupling, the ninhydrin test was negative. Removal of the Fmoc group and washings were carried out as described in the Supporting Information. Alloc-Val-OH (502 mg, 2.5 mmol, 5 equiv) was coupled using DIPCDI (387 mg, 2.5 mmol, 5 equiv) in the presence of DMAP (30.6 mg, 0.25 mmol, 0.5 equiv) and DIPEA (88 µL, 0.5 mmol, 1 equiv) for 45 min. This coupling was repeated under the same conditions twice. An aliquot of the peptidyl-resin was treated with TFA, and the HPLC results (tR ) 7.8 min, conditions S, column D) of the crude product obtained after evaporation showed a purity of >98%. ESMS, calcd for C45H63N5O11, 849.45. Found: m/z 850.1 [M + H]+. Step 3 of 7. Fmoc-D-Val-D-Pro-Orn(Boc)-D-allo-Ile-D-alloThr(Val-Alloc)-D-allo-Ile-D-Val-O-TrtCl-Resin. The Fmoc group was removed from the peptidyl-resin obtained in step 2 using piperidine/DMF 20:80 for 1 × 1 min, 2 × 5 min, 1 × 10 min, and Fmoc-Orn(Boc)-OH (912 mg, 2 mmol, 4 equiv), Fmoc-D-Pro-OH (843 mg, 2.5 mmol, 5 equiv), and Fmoc-D-Val-OH (255 mg, 2.5 mmol, 5 equiv) were sequentially incorporated using DIPCDI (310 µL, for 2.0 mmol and 4 equiv; 388 µL, for 2.5 mmol and 5 equiv) and HOBt (307 mg, for 2.0 mmol and 4 equiv; 395 mg, for 2.5 mmol and 5 equiv) for 90 min. The ninhydrin test after incorporation of Orn and D-Pro was negative. The chloranil test after incorporation of D-Val was slightly positive, and this residue was recoupled with Fmoc-D-Val-OH (678 mg, 2.0 mmol, 4 equiv), DIPCDI (310 µL, 2.0 mmol, 4 equiv) and HOBt (307 mg, 2.0 mmol, 4 equiv) for 90 min. An aliquot of the peptidyl-resin was treated with TFA, and the HPLC results (tR ) 10.1 min, conditions S, column D) of the crude product obtained after evaporation showed a purity of >98%. MALDI-TOF-MS, calcd for C65H97N9O16, 1,259.71. Found: m/z 1282.16 [M + Na]+. Step 4 of 7. (4S)-MeHex-D-Val-Thr(tBu)-Val-D-Val-D-ProOrn(Boc)-D-allo-Ile-D-allo-Thr(Val-Alloc)-D-allo-Ile-D-Val-OTrtCl-resin. The Fmoc group was removed, and Fmoc-Val-OH (678 mg, 2 mmol, 4 equiv), Fmoc-Thr(tBu)-OH (992 mg, 2.5 mmol, 5 equiv), Fmoc-D-Val-OH (678 mg, 2 mmol, 4 equiv), and (4S)MeHex-OH (195 mg, 1.5 mmol, 3 equiv) were added sequentially to the peptidyl-resin (step 3) using DIPCDI (233 µL, for 1.5 mmol


and 3 equiv; 310 µL, for 2 mmol and 4 equiv; 388 µL, for 2.5 mmol and 5 equiv) and HOBt (230 mg, for 1.5 mmol and 3 equiv; 307 mg, for 2 mmol and 4 equiv; 395 mg, 2.5 mmol and 5 equiv) for 90 min. In all cases, after 90 min of coupling, the ninhydrin test was negative. Removal of the Fmoc group and washings were carried out as described in the general procedures section. Step 5 of 7. (4S)-MeHex-D-Val-Thr(tBu)-Val-D-Val-D-ProOrn(Boc)-D-allo-Ile-D-allo-Thr(Val-Z-Dhb-Phe-Alloc)-D-allo-IleD-Val-O-TrtCl-resin. The Alloc group was removed with Pd(PPh3)4 (58 mg, 0.05 mmol, 0.1 equiv) in the presence of PhSiH3 (617 µL, 5 mmol, 10 equiv) under Ar atmosphere, and Alloc-PheZ-Dhb-OH (666 mg, 2 mmol, 4 equiv) and HOAt (273 mg, 2 mmol, 4 equiv) were dissolved in DMF (1.25 mL) and added to the peptidyl-resin. DIPCDI (310 µL, 2 mmol, 4 equiv) was then added, and the mixture was stirred for 5 h, after which the ninhydrin test was negative. After washings with DMF and CH2Cl2, an aliquot of the peptidyl-resin was treated with TFA-H2O (1:99) for 1 min and the product was characterized by MALDI-TOF-MS, calcd for C88H146N14O21, 1735.08. Found: m/z 1758.67 [M + Na]+, 1,774.62 [M + K]+. Step 6 of 7. (4S)-MeHex-D-Val-Thr(tBu)-Val-D-Val-D-ProOrn(Boc)-D-allo-Ile-D-allo-Thr(Val-Z-Dhb-Phe-H)-D-allo-Ile-DVal-OH. After washings with DMF and CH2Cl2, the Alloc group was removed with Pd(PPh3)4 (58 mg, 0.05 mmol, 0.1 equiv) in the presence of PhSiH3 (617 µL, 5 mmol, 10 equiv) under Ar atmosphere. The protected peptide was cleaved from the resin by TFA-CH2Cl2 (1:99) (5 × 30 s). Filtrate was collected on H2O (4 mL), and the H2O was partially removed under reduced pressure, appearing as a light-yellow precipitation in the remaining water. Acetonitrile was then added to dissolve the solid that appeared during H2O removal until the solution was clear. Then lyophilization gave 639 mg (387 µmol, 77% yield) of the title compound with a purity of >95% as shown by HPLC (condition R, column C, tR ) 10.5 min). Step 7 of 7. (4S)-MeHex-D-Val-Thr-Val-D-Val-D-Pro-Orn-Dallo-Ile-cyclo(D-allo-Thr-D-allo-Ile-D-Val-Phe-Z-Dhb-Val). The protected peptide from step 6 (639 mg, 387 µmol) was dissolved in CH2Cl2 (390 mL, 1 mM). Then we added compounds in the following order: HOBt (237 mg, 1.55 mmol) dissolved in the minimum volume of DMF, DIPEA (203 µL, 1.16 mmol, 2.3 equiv), and DIPCDI (240 µL, 1.55 mmol, 4 equiv). The mixture was stirred for 1 h, and the course of the cyclization step was monitored by HPLC. The solvent was removed by evaporation under reduced pressure. The protected cyclic peptide was dissolved in TFA-H2O (19:1, 85 mL), and the mixture was stirred for 1 h. The solvent was removed by evaporation under reduced pressure, dioxane was added (30 mL), and the solvent was removed by evaporation under reduced pressure (the process was repeated three times). H2O (40 mL) was then added, and the solution was lyophilized. The crude product was purified by HPLC (Kromasil C8 5 µm, 205 mm × 50 mm), isocratic 44% acetonitrile (+0.05% TFA) in water (+0.05% TFA), 55 mL/min, detection at 220 nm, to give the title product (192 mg, 0.13 mmol, 26% yield, 92.3%). HRMS m/z: found (M + H)+ 1477.937 91, calcd for C75H125N14O16 (M + H)+ 1477.939 25. The 1H NMR (2.5 mM, 500 MHz, H2O-D2O (9:1) data of the compound are shown in Table 6. Bioassays for Antitumoral Screening. Since activity data had been collected over several months, the activity value of each compound was normalized using the activity of KF on the assay day and the mean KF activity. Assay A. The objective of this assay is to interrupt the growth of an in vitro tumor cell culture by means of continued exposure of the cells to the sample to be tested. Cancer cell lines used are listed in Table 7. Inhibition of Cell Growth by Colorimetric Assay. A colorimetric type of assay using the sulforhodamine B reaction was adapted for quantitative measurement of cell growth and viability.21 This assay employed 96-well cell culture microplates of 9 mm diameter.22,23 Most of the cell lines were obtained from American Type Culture Collection (ATCC) derived from a range of types of human cancer. Cells were maintained in RPMI 1640 10% FBS,


Jiménez et al.

Table 6. [4(S)-MeHex14]KF (Compound 100) 1H NMR Chemical Shifts residue

N-H

(Z)-Dhb D-allo-Ile 1 L-Phe D-allo-Thr D-Val 3 L-Orn D-allo-Ile 2 D-Val 5 L-Thr D-Val 2 L-Val 4 L-Val 1 D-Pro 4(S)-MeHex

9.59 (s) 8.82 (d, J ) 9.0 Hz) 8.75 (d, J )5.5 Hz) 8.67(d, J ) 9.0 Hz) 8.13 (d, J ) 7.5 Hz) 8.29 (d, J ) 7.5 Hz) 7.92 (d) 8.01 (d) 8.19 (d, J ) 7.5 Hz) 7.89 (d, J ) 7.5 Hz) 8.04 (d) 7.19 (d, J ) 9.0 Hz)

HR 4.42 4.63 4.64 4.33 4.31 4.18 4.08 4.29 4.32 4.10 4.02 4.36 2.26 (2H)

Hβ

other

6.63 (q, J )7.5 Hz) 1.19 (d, γ-CH3) 1.87 1.25, 1.09, 0.82 (γ-CH2, γ-CH3, δ-CH3) 3.08 (m) 7.31 (2H Ar, t), 7.25 (3H Ar, d) 5.05 (m) 1.21 (γ-CH3) 2.01 0.90 (2 γ -CH3) 1.66 (2H) 1.88 (γ-CH2), 2.96 (bs, δ-CH2), 7.56 (ε-NH3+) 1.80 1.25, 1.09, 0.81 (γ-CH2, γ-CH3, δ-CH3) 2.07 0.87 (2 γ-CH3) 4.14 (m) 1.13 (γ-CH3) 2.11 0.78 (γ-CH3) 2.07 0.90 (2 γ-CH3) 1.52 0.75 (γ-CH3), 0.65 (d, γ-CH3) 2.23, 1.99 (m, β-CH2), 1.85 (m, γ-CH2), 3.83 (1H, m, δ-CH2), 3.64 (1H, m, δ-CH2) 1.57 (β-CH2), 1.26, 1.10, 1.33, 0.79 (δ-CH2, δ-CH3, γ-CH, ε-CH3)

Table 7. Cellular Lines Used in Assay A name

no. ATCC

species

tissue

description

DU-145 LN-caP IGROV IGROV-ET SK-BR-3 MEL-28 A-549 K-562 PANC-1 HT-29 LoVo LoVo-Dox HELA HELA-APL

HTB-81 CRL-1740

human human human human human human human human human human human human human human

prostate prostate ovary ovary breast melanoma lung bone marrow; pancreas colon colon colon cervix cervix

prostate carcinoma, not androgen receptors prostate adenocarcinoma, with androgen receptors ovary adenocarcinoma ovary adenocarcinoma, characterized as ET-743 resistant cells breast adenocarcinoma, Her2/neu+, (pleural effusion) malignant melanoma lung carcinoma ”NSCL” chronic myelogenous leukemia pancreatic epitheloid carcinoma colon adenocarcinoma colon adenocarcinoma colon adenocarcinoma (MDR) cervix epitheloid carcinoma cervix epitheloid carcinoma, characterized as aplidine resistant cells

HTB-30 HTB-72 CCL-185 CCL-243 CRL-1469 HTB-38 CCL-229 CCL-2 CCL-3

supplemented with 0.1 g/L penicillin and 0.1 g/L streptomycin sulfate and then incubated at 37 °C, 5% CO2, and 98% humidity. For the experiments, cells were harvested from subconfluent cultures using trypsin and resuspended in fresh medium before plating. Cells were seeded in 96-well microtiter plates, at 5 × 103 cells per well in aliquots of 195 µL medium, and allowed to attach to the plate surface by growing in drug-free medium for 18 h. Afterward, samples were added in aliquots of 5 µL in a range between 10 and 8 µg/mL, and dissolved in DMSO/EtOH/PBS (0.5:0.5:99). After 48 h of exposure, the antitumor effect was measured by the sulforhodamine B (SRB) methodology: cells were fixed by adding 50 µL of cold 50% (wt/vol) trichloroacetic acid and then incubated for 60 min at 4 °C. Plates were washed with deionized water and dried. An amount of 100 µL of SRB solution (0.4 wt %/vol in 1% acetic acid) was added to each microtiter well and incubated for 10 min at room temperature. Unbound SRB was removed by washing with 1% acetic acid. Plates were air-dried, and the bound stain was solubilized with Tris buffer. Optical densities were read on an automated spectrophotometric plate reader at a single wavelength of 490 nm. The values for mean ( SD of data from triplicate wells were calculated. Some parameters for cellular responses were calculated: GI ) growth inhibition, TGI ) total growth inhibition (cytostatic effect), and LC ) cell killing (cytotoxic effect). Assay B. This assay used 24-well multidishes of 16 mm in diameter. The tumor cell lines employed were A-549 (ATCC CCL 185) (monolayer culture of a human lung carcinoma), HT-29 (ATCC HTB-38) (monolayer culture of a human colon carcinoma), MEL-28 (ATCC HTB-72) (monolayer culture of a human melanoma), and DU-145 (ATCC HBTB-81) (monolayer culture of a human prostate carcinoma). Cells were maintained in the logarithmic phase of growth in Eagle’s minimum essential medium, with Earle’s balanced salts, with nonessential amino acids, with 2.0 mM L-glutamine, without sodium bicarbonate (EMEM/neaa), supplemented with 10% fetal calf serum (FSC), 10-2 M sodium bicarbonate, and 0.1 U/L penicillin G + 0.1 g/L streptomycin sulfate. For the experiments,

cells were harvested from subconfluent cultures using trypsin and resuspended in fresh medium before plating. A-549, HT-29, MEL-28, and DU-145 cells were seeded into 16mm diameter wells at 1 × 104 cells per well in 1 mL aliquots of EMEM 5% FCS containing a range of concentrations of the sample to be tested. A separate set of cultures without drug was seeded as control of growth to ensure that cells remained in an exponential phase of growth. All determinations were carried out in duplicate. After 3 days of incubation at 37 °C, 5% CO2 in a 98% humid atmosphere, cells were stained with 0.1% crystal violet. An approximate IC50 was determined by comparing the growth in wells containing the drug to the growth in control wells. For quantification of the activity, after the incubation time cells were trypsinized and counted in a Coulter counter ZM. All counts (net cells per well) represented the average of duplicate wells, % G, percent of growth relative to cultures without drug. The results of these assays were used to generate dose-response curves from which more precise IC50 values were determined (sample concentration that produces 50% cell growth inhibition). The results obtained may predict the usefulness of a certain drug as a potential cancer treatment. For this technique, compounds that showed IC50 values smaller than 1 µM were selected for further studies. IC50 data allowed us to predict that a drug not only may be cystostatic but may also provide potential benefit in terms of tumor reduction.

Acknowledgment. This study was partially supported by PharmaMar, S.A., CICYT (Grant CTQ2006-03794/BQU, PETRI), the Generalitat de Catalunya (Grant 2005SGR 00662), the ISCIII (CIBER, nanomedicine), the Institute for Research in Biomedicine, and the Barcelona Science Park. Supporting Information Available: Synthesis procedures and characterization by HPLC and MS, as well as in vitro assay data. This material is available free of charge via the Internet at http:// pubs.acs.org.


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StructureâActivity Relationship of Kahalalide F Synthetic Analogues

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StructureâActivity Relationship of Kahalalide F Synthetic Analogues